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• Illumina TSO500 RNA Dataset for Manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Illumina TSO500 RNA Dataset for Manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Dataset EGAD00001015397

• Organoid Derivation Project - GRCh38 - RNAseq (2023-06-22)

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

  Dataset EGAD00001011092

• TXT_Cytof_15B

  Matrix of normal values from 39 marker CyTOF assay performed on longitudinal BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011143

• SNF_CyTOFF_20

  Matrix of normal values from 39 marker CyTOF assay performed on baseline BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011146

• CPM table for OAK (GO28915)

  This dataset contains counts per million for 699 tumor samples profiled by RNA-seq for the entire transcriptome for samples originating from OAK (GO28915).

  Dataset EGAD00001008629

• CPM table for POPLAR (GO28953)

  This dataset contains counts per million for 192 tumor samples profiled by RNA-seq for the entire transcriptome for samples originating from POPLAR (GO28753).

  Dataset EGAD00001008631

• Log2 normalized TPM matrix for POPLAR (GO28753)

  This dataset contains log2(TPM + 1) for 192 tumor samples profiled by RNA-seq for the entire transcriptome for samples originating from POPLAR (GO28753).

  Dataset EGAD00001008390

• Log2 normalized TPM matrix for OAK (GO28915)

  This dataset contains log2(TPM + 1) for 699 tumor samples profiled by RNA-seq for the entire transcriptome for samples originating from OAK (GO28915).

  Dataset EGAD00001008391

• ChIP-seq in colorectal cancer and paired adjacent normal mucosa

  Chip-seq samples for 20 colorectal patients with paired adjacent normal mucosa to characterize H3K27ac and H3K4me1.

  Study EGAS00001005303

• International consensus definition of DNA methylation subgroups in juvenile myelomonocytic leukemia

  Known clinical and genetic markers have limitations in predicting disease course and outcome in juvenile myelomonocytic leukemia (JMML). DNA methylation (DNAme) patterns in JMML have correlated with outcome across multiple studies, suggesting it as a biomarker to improve patient stratification. However, standardized approaches to classify JMML based on DNAme patterns are lacking. We therefore sought to define an international consensus for DNAme subgroups in JMML and develop classification methods for clinical implementation.

  Study EGAS00001004682

• Brain mets discovery cohort copy number calls

  These are the Sequenza copy number calls for the 30 brain tumour samples within the discovery cohort.

  Dataset EGAD00001005983

• Charles University - Hemminki Lab DAC

  Charles University DAC is described at: https://cuni.cz/UKEN-1958.html#:~:text=Data%20sharing,%2C%20as%20closed%20as%20necessary%E2%80%9D

  Dac EGAC50000000393

• DAC Therapeutic vulnerabilities in the DNA damage response for the treatment of ATRX mutant neuroblastoma

  Dac EGAC00001001675

• 13K T2D-GENES analysis files

  This data set includes the following summary level data files used for the 13k analysis of T2D-GENES data: wes.variants.list: list of variants to keep for any analysis of the exomes data wes.assoc.samples.list: list of samples to keep for association analysis wes.assoc.variants.list: list of variants to keep for association analysis wes.sv.assoc.txt: single variant association analysis results wes.gene.ptv.variants.list.txt: list of protein truncating variants to use in gene-level analysis wes.gene.ptv.assoc.txt: results from gene-level tests of protein truncating variants wes.gene.nsstrict.variants.list.txt: list of NSstrict variants to use in gene-level analysis wes.gene.nsstrict.assoc.txt: results from gene-level tests of NSstrict variants wes.gene.nsbroad.variants.list.txt: list of NSbroad variants to use in gene-level analysis wes.gene.nsbroad.assoc.txt: results from gene-level tests of NSbroad variants wes.gene.ns.variants.list.txt: list of non synonymous variants to use in gene-level analysis wes.gene.ns.assoc.txt: results from gene-level tests of non synonymous variants

  Dataset EGAD00010001188

• Human_Developmental_Cell_Atlas_HDCA___WGS

  Single cell + bulk genomics study for immune and hematopoietic organs during human fetal development

  Study EGAS00001002929

• Ewing's sarcoma sequencing data

  This study shares DNA and RNA sequencing data for patients with Ewing's sarcoma

  Study EGAS00001005689

• Dac for "Combined single-cell transcriptomics and T-cell receptor sequencing reveal heterogeneity of mycosis fungoides between and within patients and identify a CD4+ cytotoxic subtype"

  Dac for "Combined single-cell transcriptomics and T-cell receptor sequencing reveal heterogeneity of mycosis fungoides between and within patients and identify a CD4+ cytotoxic subtype" with Name: Menghong Yin Email address: menghong.yin@dkfz-heidelberg.de Associated affiliation: Translational Skin Cancer Research Lab (DKFZ)

  Dac EGAC50000000168

• Fastq data for whole genome shotgun sequencing for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for whole genome shotgun sequencing assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001400

• Fastq data for stranded mRNA-Seq assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for stranded mRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001402

• Fastq data for ChIP-Seq (H3K27ac) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (H3K27ac) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001403

• Fastq data for ChIP-Seq (H3K27me3) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (H3K27me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001404

• Fastq data for ChIP-Seq (H3K36me3) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (H3K36me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001405

• Fastq data for ChIP-Seq (H3K4me1) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (H3K4me1) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001406

• Fastq data for ChIP-Seq (H3K4me3) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (H3K4me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001407

• cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Raw data for cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Study EGAS50000001539

• Whole-genome sequencing for 61 early-onset diabetes patients and 174 controls

  This dataset contains 241 paired FASTQ files for 61 early-onset diabetes patient and 174 controls sequenced with MGI Tech DNBSEQ-T10 and DNBSEQ-T7.

  Dataset EGAD50000001450

• Chip-exo and Chip-nexus for five TFs in three colorectal cancer cell lines

  Chip-exo and Chip-nexus for FOXA1, HNF4A, KLF5, MYC, and TCF7L2 in colorectal cancer cell lines LoVo, GP5D, COLO320DM

  Dataset EGAD00001004099

• COVID-19 Severity of First Wave of Infection for Severe Patients in Madrid

  Through thorough exclusion criteria and deep phenotypic characterisation for a Madrid-based population we intend to find enrichment of gene mutations associated to severity. In addition we will look for statistically overrepresented annotation of particular phenotypes (a controlled vocabulary specifically developed for this project) that associate them to affected genes in our patient sample.

  Study EGAS00001005931

• MutationalPatterns2: The one stop shop for the analysis of mutational processes: DNA repair deletions

  Study EGAS00001004789

• Array data for oesophageal and related samples - aks_paper_methyl_barretts_release

  Array data for oesophageal and related samples - aks_paper_methyl_barretts_release

  Dataset EGAD00010001972

• Validation_for_human_early_embryonic_substitutions_

  PCR and MiSeq validation for early embryonic substitution candidates from 400 Breast cancer patients

  Study EGAS00001001218

• Acute myeloid leukemia sequencing data

  This study contains tumor DNA and RNA sequencing data for 1 AML patient

  Study EGAS00001006354

• Dataset for "Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration" (pacBio)

  Dataset for "Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration" (pacBio)

  Dataset EGAD00001009631

• Dataset for "Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration" (ONT)

  Dataset for "Intratumoral Heterogeneity and Clonal Evolution Induced by HPV Integration" (ONT)

  Dataset EGAD00001009632

• Whole exome sequencing data for paired non-serous endometrial and ovarian carcinomas from 27 patients with concurrent tumours.

  Dataset for Synchronous Endometrial and Ovarian Cancer

  Dataset EGAD00001015680

• RNA-Seq data for Academic and For-Profit researchers.

  RNA-Seq data for both Academic and For-profit use

  Dataset EGAD00001009676

• Stitched BAM files for manuscript titled Discrepancies in Tumour Mutation Burden (TMB) reporting from sequential Endobronchial ultrasound trans bronchial needle aspiration (EBUS TBNA) samples within single lymph node stations for SNP and INDEL Variant Calling.

  Stitched BAM files for manuscript titled Discrepancies in Tumour Mutation Burden (TMB) reporting from sequential Endobronchial ultrasound trans bronchial needle aspiration (EBUS TBNA) samples within single lymph node stations for SNP and INDEL Variant Calling.

  Dataset EGAD00001012639

• DNA Whole Exome Sequence for manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  DNA Whole Exome Sequence for manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Dataset EGAD00001015395

• Circulating immune cell landscape in colorectal cancer patients

  To understand the circulating immune cells in colorectal cancer patients, we performed single-cell RNA sequencing for 14 PBMC samples from 14 colorectal cancer patients.

  Study EGAS50000000590

• Investigating transcriptional changes in rapidly differentiated iPSC-derived neurons (i3Ns) harbouring the SNCA A53T mutation +/- RSL3

  In this study we performed bulk RNA sequencing of a iPSC-derived rapid neuronal model harbouring the Parkinson's disease associated A53T mutation in SNCA. These neurons were subsequently treated with a low dose of RSL3 (300nM) for 6 hours to establish the transcriptional impact of ferroptosis induction in the presence or absence of SNCA A53T mutation.

  Study EGAS50000001536

• Tumor heterogeneity and immune-evasive microenvironment in T follicular helper cell lymphomas

  Single-cell analysis data for tumor and immune cells from lymph node and peripheral blood samples of 14 patients with T follicular helper cell lymphomas

  Study EGAS50000000275

• University Clinic Golnik DAC

  DAC of the University Clinic Golnik, that will decide regarding the requests for data submitted on behalf of research groups of the Clinic

  Dac EGAC50000000820

• Circulating cell-free DNA methylation profiling for detection, distinction, and estrogen receptor status classification of advanced breast cancer

  We developed cell-free DNA (cfDNA) methylation signatures for minimally invasive breast cancer detection, distinction, and estrogen receptor (ER) status classification with cell-free Methylated DNA Immunoprecipitation and Sequencing (cfMeDIP-seq). We profiled peripheral blood plasma from 87 patients with mBC spanning ER-positive/HER2-negative (ER+/HER2-), HER2-positive, and triple-negative breast cancer (TNBC).

  Study EGAS50000001675

• WES and WGS data for HGSC patient derived cell lines and fresh frozen tumor samples from same patients

  Sequencing data for three HGSC patients with patient derived cell lines. WES data for two patient derived cell line samples and matched blood control samples. Fresh frozen tumor samples of two patients with WES or WGS sequencing data.

  Dataset EGAD00001009330

• Integrated Metabolic Profiling and Gene Expression Analysis Reveals Therapeutic Modalities in Breast Cancer

  In this study, we performed metabolite profiling and RNA-sequencing on human breast cancer tumors and normal breast tissue samples, including triple negative breast cancer (TNBC), estrogen receptor positive breast cancer (ER+) and paired normal samples, and patient-derived xenografts (PDX) samples. Here, we report two distinctive groups defined by metabolites; a TNBC-HIGH group that shows high levels of pyrimidine pathway metabolites and biosynthetic enzymes, and an ER-HIGH group that shows high levels of fatty acid and arginine biosynthesis intermediates. We identify different metabolic enrichment profiles between cell lines grown in vitro vs. in vivo; cell lines grown in vivo recapitulate patient tumors metabolic profiles. Further, we identify a subset of genes that strongly correlates with the TNBC-HIGH metabolic profile using integrated metabolic and gene expression profiling, which strongly predicts patient prognosis when tested on larger human datasets. As a proof-of-principle, when we target TNBC-HIGH metabolic dysregulation with a pyrimidine biosynthesis inhibitor (Brequinar), and/or a glutaminase inhibitor (CB-839), we observe therapeutic efficacy and decreased tumor growth in representative TNBC cell lines, murine p53-null mammary tumors, and in vivo patient-derived xenografts (PDXs) upon multi-agent drug treatment. This study highlights potential new therapeutic opportunities in breast cancers guided by a genomic biomarker, which could prove impactful for breast cancers that rapidly proliferate.

  Study phs002396

• Array data for oesophageal and related samples – kno_paper_methyl_release

  Array data for oesophageal and related samples – kno_paper_methyl_release

  Dataset EGAD00010001795

• Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections

  Technologies to study localized host-pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host-pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.

  Study EGAS00001006186

• NIHR BioResource Rare Diseases WGS project - Bleeding, Thrombotic and Platelet Disorders (BPD) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Bleeding, Thrombotic and Platelet Disorders (BPD) Rare Disease domain

  Dataset EGAD00001004519

• NIHR BioResource Rare Diseases WGS project - Neurological and Developmental Disorders (NDD) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Neurological and Developmental Disorders (NDD) Rare Disease domain

  Dataset EGAD00001004522

• Analysis_of_somatic_mutations_in_normal_blood__AML_and_MDS_samples

  Targeted pulldown of genes known to be recurrently mutated in AML & MDS from patient and normal samples using Agilent Sureselect and for some cases also using Illumina Truseq technology.

  Study EGAS00001000525